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cazy-parser

A way to extract specific information from the Carbohydrate-Active enZYmes.

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Make sure to visit and cite the CAZy website!

  • http://www.cazy.org/
  • Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The Carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. [PMID: 24270786].

License: GNU GPLv3

RV Honorato. CAZy-parser a way to extract information from the Carbohydrate-Active enZYmes Database. The Journal of Open Source Software, 1(8), dec 2016.

doi: 10.21105/joss.00053

Recommendation

cazy_webscraper provides broader functionality by integrating CAZy data with external resources (protein sequences, taxonomy, and structures) to build comprehensive local databases for large-scale analyses. It also includes additional features for taxonomic exploration and structural analysis that aren't available here.

Introduction

cazy-parser is a tool that extract information from CAZy in a more usable and readable format. Firstly, a script reads the HTML structure and creates a mirror of the database as a tab delimited file. Secondly, information is extracted from the database according to user inputted parameters and presented to the user as a set of accession codes.

Install / Upgrade

pip install --upgrade cazy-parser

Usage (internet connection required)

cazy-parser -h
usage: cazy-parser [-h] [-f FAMILY] [-s SUBFAMILY] [-c CHARACTERIZED] [-v] {GH,GT,PL,CA,AA}

positional arguments:
  {GH,GT,PL,CA,AA}

optional arguments:
  -h, --help            show this help message and exit
  -f FAMILY, --family FAMILY
  -s SUBFAMILY, --subfamily SUBFAMILY
  -c CHARACTERIZED, --characterized CHARACTERIZED
  -v, --version         show version

Example

Extract all fasta sequences from family 43 of Glycoside Hydrolase subfamily 1

$ cazy-parser GH -f 43 -s 1
 [2022-05-26 16:39:21,511 91 INFO] ------------------------------------------
 [2022-05-26 16:39:21,511 92 INFO]
 [2022-05-26 16:39:21,511 93 INFO] ┌─┐┌─┐┌─┐┬ ┬   ┌─┐┌─┐┬─┐┌─┐┌─┐┬─┐
 [2022-05-26 16:39:21,511 94 INFO] │  ├─┤┌─┘└┬┘───├─┘├─┤├┬┘└─┐├┤ ├┬┘
 [2022-05-26 16:39:21,511 95 INFO] └─┘┴ ┴└─┘ ┴    ┴  ┴ ┴┴└─└─┘└─┘┴└─ v2.0.1
 [2022-05-26 16:39:21,511 96 INFO]
 [2022-05-26 16:39:21,511 97 INFO] ------------------------------------------
 [2022-05-26 16:39:21,511 183 INFO] Fetching links for Glycoside-Hydrolases, url: http://www.cazy.org/Glycoside-Hydrolases.html
 [2022-05-26 16:39:22,454 189 INFO] Only using links of family 43 subfamily 1
 [2022-05-26 16:39:23,029 26 INFO] Dowloading 1415 fasta sequences...
 [2022-05-26 16:40:32,187 51 INFO] Dumping fasta sequences to file GH43_1_26052022.fasta

This will generate the following file GH43_1_DDMMYYY.fasta containing the fasta sequences.

To-do and how to contribute

Please refer to CONTRIBUTING 🤓